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- PDB-2yvh: Crystal structure of the operator-binding form of the multi-drug ... -

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Basic information

Entry
Database: PDB / ID: 2yvh
TitleCrystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR
Components
  • 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*DA)-3'
  • 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*DC)-3'
  • Transcriptional regulator
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / helix-turn-helix / TetR-family / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
TetR transcriptional regulator CgmR-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsItou, H. / Shirakihara, Y. / Tanaka, I.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of the Multidrug Binding Repressor Corynebacteriumglutamicum CgmR in Complex with Inducers and with an Operator
Authors: Itou, H. / Watanabe, N. / Yao, M. / Shirakihara, Y. / Tanaka, I.
History
DepositionApr 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator
D: Transcriptional regulator
E: 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*DC)-3'
F: 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*DA)-3'
G: 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*DC)-3'
H: 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*DA)-3'


Theoretical massNumber of molelcules
Total (without water)99,0118
Polymers99,0118
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15750 Å2
ΔGint-106.5 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.011, 80.095, 87.056
Angle α, β, γ (deg.)108.98, 102.25, 96.14
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 8 - 171 / Label seq-ID: 8 - 171

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2

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Components

#1: Protein
Transcriptional regulator / Bacterial regulatory protein / TetR family


Mass: 20472.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC13032 / Gene: cgl2612 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NMG3
#2: DNA chain 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*DC)-3'


Mass: 4224.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Sequence found in the C.glutamicum genome.
#3: DNA chain 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*DA)-3'


Mass: 4335.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Sequence found in the C.glutamicum genome.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.05M Tris-HCl, 0.1M CaCl2, 4% PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCl11
2CaCl211
3PEG 40011
4HOH11
5CaCl212
6PEG 40012
7HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97909 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2006 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 32512 / Num. obs: 32512 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.48 / Num. unique all: 3252 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→10 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.039 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.757 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25854 1595 5 %RANDOM
Rwork0.22023 ---
obs0.22213 30388 98.23 %-
all-31983 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.419 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0.32 Å2-3.16 Å2
2---1.41 Å2-0.8 Å2
3----1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 1136 0 3 6669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216926
X-RAY DIFFRACTIONr_angle_refined_deg2.1652.1859656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88324.118272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.50415982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3371540
X-RAY DIFFRACTIONr_chiral_restr0.1330.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024856
X-RAY DIFFRACTIONr_nbd_refined0.2530.23044
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.24
X-RAY DIFFRACTIONr_mcbond_it1.0971.53533
X-RAY DIFFRACTIONr_mcangle_it1.80925574
X-RAY DIFFRACTIONr_scbond_it2.42234235
X-RAY DIFFRACTIONr_scangle_it3.6264.54082
Refine LS restraints NCS

Dom-ID: 1 / Number: 1323 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.290.5
2Bmedium positional0.270.5
1Amedium thermal0.882
2Bmedium thermal0.872
LS refinement shellResolution: 2.5→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 124 -
Rwork0.32 2072 -
obs-2072 96.36 %

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